mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Some history sharing cleanup and a fix for job error reports.
This commit is contained in:
Greg Von Kuster
@@ -17,7 +17,7 @@ GALAXY TOOL ERROR REPORT
|
||||
------------------------
|
||||
|
||||
This error report was sent from the Galaxy instance hosted on the server
|
||||
"${remote_hostname}"
|
||||
"${host}"
|
||||
-----------------------------------------------------------------------------
|
||||
This is in reference to output dataset ${dataset_id}.
|
||||
-----------------------------------------------------------------------------
|
||||
@@ -65,10 +65,10 @@ class DatasetInterface( BaseController ):
|
||||
dataset = model.HistoryDatasetAssociation.get( id )
|
||||
job = dataset.creating_job_associations[0].job
|
||||
# Get the name of the server hosting the Galaxy instance from which this report originated
|
||||
remote_hostname = trans.request.remote_hostname
|
||||
host = trans.request.host
|
||||
# Build the email message
|
||||
msg = MIMEText( string.Template( error_report_template )
|
||||
.safe_substitute( remote_hostname=remote_hostname,
|
||||
.safe_substitute( host=host,
|
||||
dataset_id=dataset.id,
|
||||
email=email,
|
||||
message=message,
|
||||
|
||||
@@ -310,8 +310,9 @@ class HistoryController( BaseController ):
|
||||
email=email,
|
||||
send_to_err=send_to_err )
|
||||
if params.get( 'share_button', False ):
|
||||
can_change, cannot_change, no_change_needed, send_to_err = \
|
||||
self._populate_restricted( trans, user, histories, send_to_users, None, send_to_err )
|
||||
# The user has not yet made a choice about how to share, so dictionaries will be built for display
|
||||
can_change, cannot_change, no_change_needed, unique_no_change_needed, send_to_err = \
|
||||
self._populate_restricted( trans, user, histories, send_to_users, None, send_to_err, unique=True )
|
||||
if can_change or cannot_change:
|
||||
return trans.fill_template( "/history/share.mako",
|
||||
histories=histories,
|
||||
@@ -319,7 +320,7 @@ class HistoryController( BaseController ):
|
||||
send_to_err=send_to_err,
|
||||
can_change=can_change,
|
||||
cannot_change=cannot_change,
|
||||
no_change_needed=no_change_needed )
|
||||
no_change_needed=unique_no_change_needed )
|
||||
if no_change_needed:
|
||||
return self._share_histories( trans, user, send_to_err, histories=no_change_needed )
|
||||
elif not send_to_err:
|
||||
@@ -335,7 +336,8 @@ class HistoryController( BaseController ):
|
||||
user = trans.get_user()
|
||||
histories, send_to_users, send_to_err = self._get_histories_and_users( trans, user, id, email )
|
||||
send_to_err = ''
|
||||
can_change, cannot_change, no_change_needed, send_to_err = \
|
||||
# The user has made a choice, so dictionaries will be built for sharing
|
||||
can_change, cannot_change, no_change_needed, unique_no_change_needed, send_to_err = \
|
||||
self._populate_restricted( trans, user, histories, send_to_users, action, send_to_err )
|
||||
# Now that we've populated the can_change, cannot_change, and no_change_needed dictionaries,
|
||||
# we'll populate the histories_for_sharing dictionary from each of them.
|
||||
@@ -408,13 +410,13 @@ class HistoryController( BaseController ):
|
||||
send_to_err += "%s is not a valid Galaxy user. " % email_address
|
||||
return histories, send_to_users, send_to_err
|
||||
def _populate( self, trans, histories_for_sharing, other, send_to_err ):
|
||||
# this method will populate the histories_for_sharing dictionary with the users and
|
||||
# This method will populate the histories_for_sharing dictionary with the users and
|
||||
# histories in other, eliminating histories that have already been shared with the
|
||||
# associated user. No security checking on datasets is performed.
|
||||
# If not empty, the histories_for_sharing dictionary looks like:
|
||||
# { userA: [ historyX, historyY ], userB: [ historyY ] }
|
||||
# other looks like:
|
||||
# ## { userA: {historyX : [hda, hda], historyY : [hda]}, userB: {historyY : [hda]} }
|
||||
# { userA: {historyX : [hda, hda], historyY : [hda]}, userB: {historyY : [hda]} }
|
||||
for send_to_user, history_dict in other.items():
|
||||
for history in history_dict:
|
||||
# Make sure the current history has not already been shared with the current send_to_user
|
||||
@@ -430,20 +432,22 @@ class HistoryController( BaseController ):
|
||||
elif history not in histories_for_sharing[ send_to_user ]:
|
||||
histories_for_sharing[ send_to_user ].append( history )
|
||||
return histories_for_sharing, send_to_err
|
||||
def _populate_restricted( self, trans, user, histories, send_to_users, action, send_to_err ):
|
||||
def _populate_restricted( self, trans, user, histories, send_to_users, action, send_to_err, unique=False ):
|
||||
# The user may be attempting to share histories whose datasets cannot all be accessed by other users.
|
||||
# If this is the case, the user sharing the histories can:
|
||||
# 1) action=='public': choose to make the datasets public if he is permitted to do so
|
||||
# 2) action=='private': automatically create a new "sharing role" allowing protected
|
||||
# datasets to be accessed only by the desired users
|
||||
# 3) action=='share_anyway': share only what can be shared when no permissions are changed
|
||||
# 4) action=='no_share': Do not share anything
|
||||
# In addition, the user may be sharing a history with a user with which the history was already shared
|
||||
# and it will not be shared twice.
|
||||
# This method will populate the can_change, cannot_change and no_change_needed dictionaries.
|
||||
# This method will populate the can_change, cannot_change and no_change_needed dictionaries, which
|
||||
# are used for either displaying to the user, letting them make 1 of the choices above, or sharing
|
||||
# after the user has made a choice. They will be used for display if 'unique' is True, and will look
|
||||
# like: {historyX : [hda, hda], historyY : [hda] }
|
||||
# For sharing, they will look like:
|
||||
# { userA: {historyX : [hda, hda], historyY : [hda]}, userB: {historyY : [hda]} }
|
||||
can_change = {}
|
||||
cannot_change = {}
|
||||
no_change_needed = {}
|
||||
unique_no_change_needed = {}
|
||||
for history in histories:
|
||||
for send_to_user in send_to_users:
|
||||
# Make sure the current history has not already been shared with the current send_to_user
|
||||
@@ -456,7 +460,15 @@ class HistoryController( BaseController ):
|
||||
# Only deal with datasets that have not been purged
|
||||
for hda in history.activatable_datasets:
|
||||
if trans.app.security_agent.dataset_is_public( hda.dataset ):
|
||||
# Build the dict that will show the user what doesn't need to be changed
|
||||
# The no_change_needed dictionary is a special case. If both of can_change
|
||||
# and cannot_change are empty, no_change_needed will used for sharing. Otherwise
|
||||
# unique_no_change_needed will be used for displaying, so we need to populate both.
|
||||
# Build the dictionaries for display, containing unique histories only
|
||||
if history not in unique_no_change_needed:
|
||||
unique_no_change_needed[ history ] = [ hda ]
|
||||
else:
|
||||
unique_no_change_needed[ history ].append( hda )
|
||||
# Build the dictionaries for sharing
|
||||
if send_to_user not in no_change_needed:
|
||||
no_change_needed[ send_to_user ] = {}
|
||||
if history not in no_change_needed[ send_to_user ]:
|
||||
@@ -473,28 +485,40 @@ class HistoryController( BaseController ):
|
||||
# The current user has authority to change permissions on the current dataset because
|
||||
# they have permission to manage permissions on the dataset and the dataset is not associated
|
||||
# with a library.
|
||||
if send_to_user not in can_change:
|
||||
# Build the set of histories / datasets on which the current user has authority
|
||||
# to "manage permissions".
|
||||
can_change[ send_to_user ] = {}
|
||||
if history not in can_change[ send_to_user ]:
|
||||
can_change[ send_to_user ][ history ] = [ hda ]
|
||||
if unique:
|
||||
# Build the dictionaries for display, containing unique histories only
|
||||
if history not in can_change:
|
||||
can_change[ history ] = [ hda ]
|
||||
else:
|
||||
can_change[ history ].append( hda )
|
||||
else:
|
||||
can_change[ send_to_user ][ history ].append( hda )
|
||||
# Build the dictionaries for sharing
|
||||
if send_to_user not in can_change:
|
||||
can_change[ send_to_user ] = {}
|
||||
if history not in can_change[ send_to_user ]:
|
||||
can_change[ send_to_user ][ history ] = [ hda ]
|
||||
else:
|
||||
can_change[ send_to_user ][ history ].append( hda )
|
||||
else:
|
||||
if action in [ "private", "public" ]:
|
||||
# Don't change stuff that the user doesn't have permission to change
|
||||
# The user has made a choice, so 'unique' doesn't apply. Don't change stuff
|
||||
# that the user doesn't have permission to change
|
||||
continue
|
||||
#elif send_to_user not in cannot_change:
|
||||
if send_to_user not in cannot_change:
|
||||
# Build the set of histories / datasets on which the current user does
|
||||
# not have authority to "manage permissions".
|
||||
cannot_change[ send_to_user ] = {}
|
||||
if history not in cannot_change[ send_to_user ]:
|
||||
cannot_change[ send_to_user ][ history ] = [ hda ]
|
||||
if unique:
|
||||
# Build the dictionaries for display, containing unique histories only
|
||||
if history not in cannot_change:
|
||||
cannot_change[ history ] = [ hda ]
|
||||
else:
|
||||
cannot_change[ history ].append( hda )
|
||||
else:
|
||||
cannot_change[ send_to_user ][ history ].append( hda )
|
||||
return can_change, cannot_change, no_change_needed, send_to_err
|
||||
# Build the dictionaries for sharing
|
||||
if send_to_user not in cannot_change:
|
||||
cannot_change[ send_to_user ] = {}
|
||||
if history not in cannot_change[ send_to_user ]:
|
||||
cannot_change[ send_to_user ][ history ] = [ hda ]
|
||||
else:
|
||||
cannot_change[ send_to_user ][ history ].append( hda )
|
||||
return can_change, cannot_change, no_change_needed, unique_no_change_needed, send_to_err
|
||||
def _share_histories( self, trans, user, send_to_err, histories={} ):
|
||||
# histories looks like: { userA: [ historyX, historyY ], userB: [ historyY ] }
|
||||
msg = ""
|
||||
@@ -605,6 +629,7 @@ class HistoryController( BaseController ):
|
||||
if clone_choice == 'activatable':
|
||||
new_history = history.copy( name=name, target_user=user, activatable=True )
|
||||
elif clone_choice == 'active':
|
||||
name += " (active items only)"
|
||||
new_history = history.copy( name=name, target_user=user )
|
||||
# Render the list view
|
||||
return trans.show_ok_message( 'Clone with name "%s" is now included in your list of stored histories.' % new_history.name )
|
||||
|
||||
@@ -18,7 +18,7 @@
|
||||
${history.name}
|
||||
<a id="shared-${i}-popup" class="popup-arrow" style="display: none;">▼</a>
|
||||
<div popupmenu="shared-${i}-popup">
|
||||
<a class="action-button" href="${h.url_for( controller='history', action='clone', id=trans.security.encode_id( history.id ), clone_choice='activatable' )}">Clone</a>
|
||||
<a class="action-button" href="${h.url_for( controller='history', action='clone', id=trans.security.encode_id( history.id ) )}">Clone</a>
|
||||
</div>
|
||||
</td>
|
||||
<td>${history.user.email}</td>
|
||||
|
||||
@@ -64,35 +64,14 @@
|
||||
<input type="hidden" name="id" value="${trans.security.encode_id( history.id )}">
|
||||
%endfor
|
||||
%if no_change_needed:
|
||||
## no_change_needed looks like: {historyX : [hda, hda], historyY : [hda] }
|
||||
<div style="clear: both"></div>
|
||||
<div class="form-row">
|
||||
<div class="donemessage">
|
||||
The following datasets can be shared with ${email} with no changes
|
||||
</div>
|
||||
</div>
|
||||
## no_change_needed looks like:
|
||||
## { userA: {historyX : [hda, hda], historyY : [hda]}, userB: {historyY : [hda]} }
|
||||
<%
|
||||
# TODO: move generation of these unique dictionaries to the history controller
|
||||
# Build the list of unique histories and datasets
|
||||
unique_stuff = {}
|
||||
%>
|
||||
%for user, history_dict in no_change_needed.items():
|
||||
%for history, hdas in history_dict.items():
|
||||
<%
|
||||
if history in unique_stuff:
|
||||
for hda in hdas:
|
||||
if hda not in unique_stuff[ history ]:
|
||||
unique_stuff[ history ].append( hda )
|
||||
else:
|
||||
unique_stuff[ history ] = []
|
||||
for hda in hdas:
|
||||
if hda not in unique_stuff[ history ]:
|
||||
unique_stuff[ history ].append( hda )
|
||||
%>
|
||||
%endfor
|
||||
%endfor
|
||||
%for history, hdas in unique_stuff.items():
|
||||
</div>
|
||||
%for history, hdas in no_change_needed.items():
|
||||
<div class="form-row">
|
||||
<label>History</label>
|
||||
${history.name}
|
||||
@@ -104,40 +83,22 @@
|
||||
%for hda in hdas:
|
||||
<div class="form-row">
|
||||
${hda.name}
|
||||
%if hda.deleted:
|
||||
(deleted)
|
||||
%endif
|
||||
</div>
|
||||
%endfor
|
||||
%endfor
|
||||
%endif
|
||||
%if can_change:
|
||||
## can_change looks like: {historyX : [hda, hda], historyY : [hda] }
|
||||
<div style="clear: both"></div>
|
||||
<div class="form-row">
|
||||
<div class="warningmessage">
|
||||
The following datasets can be shared with ${email} by updating their permissions
|
||||
</div>
|
||||
</div>
|
||||
## can_change looks like:
|
||||
## { userA: {historyX : [hda, hda], historyY : [hda]}, userB: {historyY : [hda]} }
|
||||
<%
|
||||
# TODO: move generation of these unique dictionaries to the history controller
|
||||
# Build the list of unique histories and datasets
|
||||
unique_stuff = {}
|
||||
%>
|
||||
%for user, history_dict in can_change.items():
|
||||
%for history, hdas in history_dict.items():
|
||||
<%
|
||||
if history in unique_stuff:
|
||||
for hda in hdas:
|
||||
if hda not in unique_stuff[ history ]:
|
||||
unique_stuff[ history ].append( hda )
|
||||
else:
|
||||
unique_stuff[ history ] = []
|
||||
for hda in hdas:
|
||||
if hda not in unique_stuff[ history ]:
|
||||
unique_stuff[ history ].append( hda )
|
||||
%>
|
||||
%endfor
|
||||
%endfor
|
||||
%for history, hdas in unique_stuff.items():
|
||||
%for history, hdas in can_change.items():
|
||||
<div class="form-row">
|
||||
<label>History</label>
|
||||
${history.name}
|
||||
@@ -149,11 +110,15 @@
|
||||
%for hda in hdas:
|
||||
<div class="form-row">
|
||||
${hda.name}
|
||||
%if hda.deleted:
|
||||
(deleted)
|
||||
%endif
|
||||
</div>
|
||||
%endfor
|
||||
%endfor
|
||||
%endif
|
||||
%if cannot_change:
|
||||
## cannot_change looks like: {historyX : [hda, hda], historyY : [hda] }
|
||||
<div style="clear: both"></div>
|
||||
<div class="form-row">
|
||||
<div class="errormessage">
|
||||
@@ -161,29 +126,7 @@
|
||||
change the permissions on them
|
||||
</div>
|
||||
</div>
|
||||
## cannot_change looks like:
|
||||
## { userA: {historyX : [hda, hda], historyY : [hda]}, userB: {historyY : [hda]} }
|
||||
<%
|
||||
# TODO: move generation of these unique dictionaries to the history controller
|
||||
# Build the list of unique histories and datasets
|
||||
unique_stuff = {}
|
||||
%>
|
||||
%for user, history_dict in can_change.items():
|
||||
%for history, hdas in history_dict.items():
|
||||
<%
|
||||
if history in unique_stuff:
|
||||
for hda in hdas:
|
||||
if hda not in unique_stuff[ history ]:
|
||||
unique_stuff[ history ].append( hda )
|
||||
else:
|
||||
unique_stuff[ history ] = []
|
||||
for hda in hdas:
|
||||
if hda not in unique_stuff[ history ]:
|
||||
unique_stuff[ history ].append( hda )
|
||||
%>
|
||||
%endfor
|
||||
%endfor
|
||||
%for history, hdas in unique_stuff.items():
|
||||
%for history, hdas in cannot_change.items():
|
||||
<div class="form-row">
|
||||
<label>History</label>
|
||||
${history.name}
|
||||
@@ -195,10 +138,17 @@
|
||||
%for hda in hdas:
|
||||
<div class="form-row">
|
||||
${hda.name}
|
||||
%if hda.deleted:
|
||||
(deleted)
|
||||
%endif
|
||||
</div>
|
||||
%endfor
|
||||
%endfor
|
||||
%endif
|
||||
<div class="toolFormTitle"></div>
|
||||
<div class="form-row">
|
||||
Deleted items can be eliminated by the users with which you are sharing the history.
|
||||
</div>
|
||||
<div class="form-row">
|
||||
<label>How would you like to proceed?</label>
|
||||
</div>
|
||||
|
||||
@@ -253,7 +253,7 @@ class TestHistory( TwillTestCase ):
|
||||
# Check list of histories to make sure shared history3 was cloned
|
||||
self.view_stored_active_histories( check_str="Clone of '%s'" % history3.name )
|
||||
# Switch to the cloned history to make sure activatable datasets were cloned
|
||||
self.switch_history( id=self.security.encode_id( history3_clone3.id ), name=history3_clone3.name )
|
||||
self.switch_history( id=self.security.encode_id( history3_clone3.id ) )
|
||||
# Make sure the deleted datasets are NOT included in the cloned history
|
||||
try:
|
||||
self.check_history_for_string( 'This dataset has been deleted.', show_deleted=True )
|
||||
|
||||
Reference in New Issue
Block a user